{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:45Z","timestamp":1772138085885,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2017,12,21]],"date-time":"2017-12-21T00:00:00Z","timestamp":1513814400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,5,15]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n Comprehensive 2D gas chromatography-mass spectrometry is a powerful method for analyzing complex mixtures of volatile compounds, but produces a large amount of raw data that requires downstream processing to align signals of interest (peaks) across multiple samples and match peak characteristics to reference standard libraries prior to downstream statistical analysis. Very few existing tools address this aspect of analysis and those that do have shortfalls in usability or performance. We have developed an R package that implements retention time and mass spectra similarity threshold-free alignments, seamlessly integrates retention time standards for universally reproducible alignments, performs common ion filtering and provides compatibility with multiple peak quantification methods. We demonstrate that our package\u2019s performance compares favorably to existing tools on a controlled mix of metabolite standards separated under variable chromatography conditions and data generated from cell lines.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n R2DGC can be downloaded at https:\/\/github.com\/rramaker\/R2DGC or installed via the Comprehensive R Archive Network (CRAN).<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx825","type":"journal-article","created":{"date-parts":[[2017,12,20]],"date-time":"2017-12-20T17:03:02Z","timestamp":1513789382000},"page":"1789-1791","source":"Crossref","is-referenced-by-count":7,"title":["R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8666-4841","authenticated-orcid":false,"given":"Ryne C","family":"Ramaker","sequence":"first","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA"},{"name":"Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emily R","family":"Gordon","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9627-0309","authenticated-orcid":false,"given":"Sara J","family":"Cooper","sequence":"additional","affiliation":[{"name":"HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,12,21]]},"reference":[{"key":"2023012713481487800_btx825-B1","doi-asserted-by":"crossref","first-page":"3058","DOI":"10.1021\/ac103308x","article-title":"Data analysis tool for comprehensive two-dimensional gas chromatography\/time-of-flight mass spectrometry","volume":"83","author":"Castillo","year":"2011","journal-title":"Anal. Chem"},{"key":"2023012713481487800_btx825-B2","doi-asserted-by":"crossref","first-page":"27.","DOI":"10.1186\/1471-2105-13-27","article-title":"Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry","volume":"13","author":"Jeong","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023012713481487800_btx825-B3","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1002\/mas.20158","article-title":"Comprehensive two-dimensional gas chromatography-mass spectrometry: a review","volume":"27","author":"Mondello","year":"2008","journal-title":"Mass Spectrom. Rev"},{"key":"2023012713481487800_btx825-B4","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1038\/nrd.2016.32","article-title":"Emerging applications of metabolomics in drug discovery and precision medicine","volume":"15","author":"Wishart","year":"2016","journal-title":"Nat. Rev. Drug Discov"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/10\/1789\/48935610\/bioinformatics_34_10_1789.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/10\/1789\/48935610\/bioinformatics_34_10_1789.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T08:48:59Z","timestamp":1674809339000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/10\/1789\/4769498"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,12,21]]},"references-count":4,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2018,5,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx825","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/179168","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,5,15]]},"published":{"date-parts":[[2017,12,21]]}}}